multiUMAP: Compute multiple UMAPs

In LabexCortexBioinformatics/LxCxUtils: Utils Function for Labex Cortex Bioinformatics Platform

Compute multiple UMAPs

Description

Will compute multiple umaps, and aggregate their dimplots in one plot. This plot can then be returned or saved as image (or both).

Usage

multiUMAP(
  seur,
  dims,
  out = TRUE,
  save = FALSE,
  add_to_object = FALSE,
  group.by = "ident",
  ncol = 3,
  pt.size = 0.5,
  file = paste0(getwd(), "/multiUMAP"),
  fig_size = "auto",
  dpi = 200,
  save_as = "png",
  verbose = TRUE
)

Arguments

seur	Seurat object to use.
dims	Dimensions to use. Must be an integer vector or list. Can be cast with a range, for example 5:10 will compute UMAPs 5, 6, 7, 8, 9, 10.
out	Whether to return the aggregated plot. Default to TRUE
save	Whether to save the aggregated plot. Default to FALSE
add_to_object	Whether to add every UMAP computed in the object. If TRUE, the UMAPs will be saved under "UMAP_dim" followed by the dimnesion (for exemple "UMAP_dim5" for dimension 5). If FALSE, the UMAPs will be computed under "temp" and then suppressed. Default to FALSE
group.by	Which column of the metadata to group cells by. Default to ident, which will take the active ident.
ncol	Number of columns in the aggregated plot. Default to 3
file	The file name and path if image is saved. Default to working_directory/multiUMAP.png
fig_size	The size of the saved image. Either "auto", which will try to use the best image size automatically, or a vector of int, the first one being the width in pixel and second one the height in pixel. Default is "auto"
dpi	The dpi of the saved image. Must be an int. Default to 200
save_as	The type of file to save. Default to "png"
verbose	Default to TRUE
pt_size	Size of points to use. Default to 0.5

Value

a gridExtra object if TRUE, else nothing

LabexCortexBioinformatics/LxCxUtils documentation built on Aug. 2, 2022, 6:23 a.m.